This invention relates an erogenous plasmid of Propionibacterium, derived from it and the use of these vectors to express (heterologous) proteins in bacteria, especially Propionibacteria. In particular transformed bacteria can be used either to produce, by fermentation, vitamin B12 or in cheese making.
Propionibacterium Gram-positive bacteria capable of producing various useful compounds in a variety of industrial processes. For example several Propionibacterium species are known to produce vitamin B12 (cobalamin) in large scale fermentation processes. Other species are used in dairy applications such as cheese where they contribute, and in many cases even are mainly responsible, for the specific flavour and texture of the cheese. Many Propionibacterium species are considered safe for inclusion, as live organisms, into food and animal feed.
To be able to fully exploit the biotechnological potential of Propionibacterium, efficient and flexible genetic engineering techniques are required. Such techniques rely on the availability of a suitable plasmid to express a protein from a heterologous gene in Propionibacterium. 
EP-A0400931 (Nippon Oil) refers to an endogenous plasmid (pTY-1) from Propionibacterium pentosaceum (ATCC 4875) but does not describe its sequence or exemplify how it may be used to express a heterologous gene.
JP 08-56673 refers to the plasmid pTY-1 for producing vitamin B12 but does not provide any evidence that the plasmid remains as a freely replicating extrachromosomal element nor that the plasmid is stable inside the transformed cells.
The invention therefore seeks to provide vectors that are more efficient than those in the prior art, and can remain extrachromosomal and/or are stable. In particular the invention aims to provide an efficient vector for the cloning or expression of Propionibacterium or foreign genomic fragments or genes into a (line 821) host strain. This may enable host specific restriction enzymes to be circumvented and thereby avoid the host treating the plasmid as a foreign polynucleotide.
Accordingly, the present invention in a first aspect provides a polynucleotide comprising a sequence capable of hybridising selectively to
(a) SEQ ID NO: 1 or the complement thereof
(b) a sequence from the 3.6 kb plasmid of Propionibacterium freudenrsichii CBS 101022;
(c) a sequence from the 3.6 kb plasmid of Propionibacterium freudenreichii CBS 101023; or
(d) a sequence that encodes a polypeptide of the invention, such as (at least part of) the amino acid sequence of SEQ ID NO: 2 or SEQ ID No: 3, or the complement thereof.
SEQ ID NO: 1 sets out the DNA sequence of the endogenous plasmid of Propionibacterium LMG 16545 which the inventors have discovered. The first coding sequence runs from nucleotide 273 to nucleotide 1184 and the predicted amino acid sequence of this coding sequence is shown in SEQ ID NO. 2. The second coding sequence runs from nucleotides 1181 to 1493 and the predicted amino acid sequence of this coding sequence is shown in SEQ ID No: 3.
The inventors screened a large collection of Propionibacterium isolates and identified two strains both harboring cryptic plasmids with a size of 3.6 kb. One of the strains is Propionibacterium freudenreichii LMG 16545 which was deposited at Centraalbureau voor Schimmolcultures (CBS), Oosterstraat 1, Postbus 273, NL-3740 AG Baarn Netherlands, in the name of Gist-brocades B. V. of Wateringseweg 1, P.O. Box 1, 2600 MA Delft, The Netherlands, on 19 Jun. 1998 under the terms of the Budapest Treaty and was given accession number CBS 101022. The other strain is Propionibacterium freudenreichii LMG 16546 which was also deposited by the same depositor 19 Jun. 1998 under the terms of the Budapest Treaty at CBS and was given accession number CBS 101023.
Through full characterization and computer assisted analysis of the nucleotide sequence of LMG 16545 the inventors have been able to identify insertion sites for foreign DNA fragments. These sites have allowed construction of plasmids that are still capable of autonomous replication in Propionibacterium. 
Surprisingly it was found that an erythromycin resistance gene from the actinomycete Saccharopolyspora erythraea is efficiently expressed in Propionibacterium and thus can be used as a selection marker for transformed cells.
Also constructed are bifunctional vectors, stably maintainable and selectable in both E. coli and Propionibacterium. This allows the use of E. coli for vector construction, as well as functional expression of homologous or heterologous genes in Propionibacterium. Vector construction using E. coli is comparatively easy and can be done quickly.
The polynucleotide of the invention may be autonomously replicating or extrachromosomal, for example in a bacterium such as a Propionibacterium.
Hence another aspect the invention provides a vector which comprises a polynucleotide of the invention.
The invention also provides a process for the preparation of a polypeptide, the process comprising cultivating a host cell transformed or transfected with a vector of the invention under conditions to provide for expression of the polypeptide.
The invention additionally provides a polypeptide which comprises the sequence set far out in SEQ ID NO: 2 or 3 or a sequence substantially homologous to that sequence, or a fragment of either sequence, or a protein encoded by a polynucleotide of the invention.
Polynucleotides
A polynucleotide of the invention may be capable of hybridising selectively with the sequence of SEQ ID NO: 1, or a portion of SEQ ID No: 1, or to the sequence complementary to that sequence or portion of the sequence. The polynucleotide of the invention may be capable of hybridising selectively to the sequence of the 3.6 kb plasmid of P. freudenreichii CBS 101022 or CBS 101023, or to a portion of the sequence of either plasmid. Typically, a polynucleotide of the invention is a contiguous sequence of nucleotides which is capable of selectively hybridizing to the sequence of SEQ ID. No: 1 or of either 3.6 kb plasmid, or portion of any of these sequences, or to the complement of these sequences or portion of any of these sequences.
A polynucleotide of the invention and the sequence of SEQ ID NO: 1, or either of the 3.6 kb plasmids, or a sequence encoding a polypeptide, or a portion of these sequences, can hybridize at a level significantly above background. Background hybridization may occur, for example, because of other polynucleotides present in the preparation. The signal level generated by the interaction between a polynucleotide of the invention and the sequence of SEQ ID NO: 1 or of either 3.6 kb plasmid, or portion of these sequences, is typically at least 10 fold, preferably at least 100 fold, as intense as interactions between other polynucleotides and the coding sequence of SEQ ID NO: 1 or of either 3.6 kb plasmid, or a sequence encoding the polypeptide, or portion of these sequences. The intensity of interaction may be measured for example, by radiolabelling the probe, e.g. with 32P. Selective hybridisation is typically achieved using conditions of medium stringency (for example 0.3M sodium chloride and 0.03M sodium citrate at about 50xc2x0 C.) to high stringency (same conditions but at about 60xc2x0 C.). Polynucleotides included in the invention can be generally at least 70%, preferably at least 80 or 90%, more preferably at least 95%, and optimally at least 98% homologous (to the sequence (a) to (d)) over a region of at least 20, preferably at least 30, for instance at least 40, 60 or 100 or more contiguous nucleotides.
Any combination of the above mentioned degrees of homology and minimum sizes may be used to define polynucleotides of the invention, with the more stringent combinations (i.e. higher homology over longer lengths) being preferred. Thus for example a polynucleotide which is at least 80% or 90% homologous over 25, preferably over 30 nucleotides forms one embodiment of the invention, as does a polynucleotide which is at least 90 or 95% homologous over 40 nucleotides.
The portions referred to above may be the coding sequences of SEQ ID No: 1 or of either 3.6 kb plasmid. Other preferred portions of SEQ ID No: 1 are the replication origin, promoter or regulatory sequences, or sequences capable of effecting or assisting autonomous replication in a host cell, such as a Propionibacterium. 
It has been found that the portion of the plasmid from the restriction site SalI to AlwNI appears to be the region that is required for replication of the plasmid. Other parts of the plasmid have been deleted and yet replication does not appear to have been adversely affected. Therefore in the invention sequence (b) and (c) can be the region delineated by the restriction sites SalI and AlwNI. This is approximately 1.7b in length. Alternatively, sequences (b) or (c) can be replaced by the sequence corresponding to nucleotides 1 to 1,800, such as 100 to 1,700, suitably 150 to 1,500, advantageously 200 to 1,300 and optimally 250 to 1,200 of SEQ. ID. No. 1. The proteins (SEQ. ID. Nos. 2 and 3) encoded by ORF1 and ORF2 respectively, are thought to both help the plasmid replicate. The plasmid replicates by the known rolling circle replication method where the original ds DNA plasmid is cut by either of the proteins which assists production of a copy of the outer strand using the inner strand as a template. The copy of the outer ring is removed and the ends joined. The host then replicates a new inner ring Using the generated outer ring as a template.
The coding sequences of the invention may be modified by nucleotide substitutions, for example from 1, 2 or 3 to 10, 25, 50 or 100 substitutions. The polynucleotides of sequence (a) to (d) may alternatively or additionally be modified by one or more insertions or deletions and/or by an extension at either or both ends. Degenerate substitution may be made and/or substitutions may be made which would result in a conservative amino acid substitution when the modified sequence is translated, for example as discussed later with relation to the polypeptides of the invention.
Polynucleotides of the invention may comprise DNA or RNA. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to polynucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine chains at the 3xe2x80x2 and/or 5xe2x80x2 ends of the molecule. For the purposes of the present invention, it is to be understood that the polynucleotide described herein may be modified by any method available in the art. Such modifications may be carried out in order to enhance in vivo activity or lifespan.
Polynucleotides of the invention may be used as a primer, e.g. a PCR (polymerase chain reaction) primer, a primer for an alternative amplification reaction, a probe e.g. labelled with a revealing label by conventional means using radioactive or non-radioactive labels, or the polynucleotides may be incorporated or cloned into vectors.
Such primers, probes and other fragments will be at least 15, preferably at least 20, for example at least 25, 30 or 40 nucleotides in length. They will typically be up to 40, 50, 60, 70, 100 or 150 nucleotides in length. Probes and fragments can be longer than 150 nucleotides, for example up to 200, 300, 500, 1,000 or 1,500 nucleotides in length, or even up to a few nucleotides, such as 5 or 10 nucleotides, short of any of the sequence (a) to (d).
Polynucleotides such as a DNA polynucleotide and primers according to the invention may be produced recombinantly, synthetically, or by any means available to those of skill in the art. They may also be cloned by standard techniques. The polynucleotides are typically provided in isolated and/or purified form.
In general, primers will be produced by synthetic means, involving a step wise manufacture of the desired nucleic acid sequence one nucleotide at a time. Techniques for accomplishing this using automated techniques are readily available in the art.
Longer polynucleotides will generally be produced using recombinant means, for example using PCR cloning techniques. This will involve making a pair of primers (e.g. of about 15-30 nucleotides) to the region of SEQ. ID No: 1 or of either 3.6 kb plasmid which it is desired to clone, bringing the primers into contact with DNA obtained from a Propionibacterium, performing a polymerase chain reaction under conditions which bring about amplification of the desired region, isolating the amplified fragment (e.g. by purifying the reaction mixture on an agarose gel) and recovering the amplified DNA. The primers may be designed to contain suitable restriction enzyme recognition sites so that the amplified DNA can be clone into a suitable cloning vector. Such techniques may be used to obtain all or part of SEQ ID No: 1 or either 3.6 kb plasmid.
The techniques mentioned herein are well known in the art10.
Polynucleotides which are not 100% homologous to SEQ ID No: 1 or either 3.6 kb plasmid but fall within the scope of the invention can be obtained in a number of ways.
Homologous polynucleotides of SEQ ID NO: 1 or of either 3.6 kb plasmid may be obtained for example by probing genomic DNA libraries made from a range of Propionibacteria, such as P. freudenreichii, P. jensenii, P. thoenii, P. acidipropiloici, or other strains of bacteria of the class Actinomycetes, or other gram positive bacteria, or those that are G: C rich. All these organisms are suitable sources of homologous or heterologous genes, promoters, enhancers, or host cells, for use in the invention.
Such homologues and fragments thereof in general will be capable of selectively hybridizing to the coding sequence of SEQ ID NO: 1 or its complement or of either 3.6 kb plasmid. Such sequences may be obtained by probing genomic DNA libraries of the Propionibacterium with probes comprising all or part of the coding sequence SEQ ID NO: 1 or of either 3.6 kb plasmid under conditions of medium to high stringency (for example 0.03M sodium chloride and 0.3M sodium citrate at from about 50xc2x0 C. to about 60xc2x0 C.).
Homologues may also be obtained using degenerate PCR which will use primers designed to target conserved sequences within the homologues. Conserved sequences can be predicted from aligning SEQ ID No: 1 or the sequence of either 3.6 kb plasmid with their homologues. The primers will contain one or more degenerate positions and will be used at stringency conditions lower than those used for cloning sequences with single sequence primers against known sequences.
Alternatively, such polynucleotides may be obtained by site directed mutagenesis of SEQ ID No: 1 or of either 3.6 kb plasmid, or their homologues. This may be useful where for example silent codon changes are required to sequences to optimise codon preferences for a particular host cell in which the polynucleotide sequences are being exposed. Other sequences may be desired in order to introduce restriction enzyme recognition sites or to alter the property or function of the polypeptides encoded by the polynucleotides.
Methods of measuring polynucleotide homology are well known in the art. For example the UWGCO package provides the BESTFIT programme which can be used to calculate homology, for example used on its default setting7. For amino acid homology with regard to polypeptides of the invention which are discussed later, one can employ BLAST (Basic Local Alignment Search Tool1), which produces alignments of amino acid sequences (and nucleotide sequences if necessary) to determine sequence similarity. BLAST can thus be used to determine exact matches or to identify homologues, and is particularly used for those matches which do not contain gaps. The BLAST technique uses the algorithm based on the High-scoring Segment Pair (HSP).
The invention includes double sided polynucleotides comprising a polynucleotide sequence of the invention and its complement.
Polynucleotides (e.g. probes or primers) of the invention may carry a revealing label. Suitable labels include radioisotopes such as 32P or 35S, enzyme labels, or other protein labels such as biotin. Detection techniques for these labels are known per se.
The polynucleotides (labelled or unlabelled) may be used in nucleic acid-based tests for detecting or sequencing another polynucleotide of the invention, in a sample.
Polynucleotides of the invention include variants of the sequence of SEQ ID 1 or of either 3.6 kb plasmid which are capable of autonomously replicating or remaining extrachromosomally in a host cell. Such variants may be stable in a bacterium such as a Propionibacterium. 
Generally the polynucleotide will comprise the replication origin and/or coding region(s) of SEQ ID No: 1 or of either 3.6 kb plasmid, or homologues of these sequences. A polynucleotide of the invention which is stable in a host cell such as Propionibacterium, or E. coli is one which is not lost from the host within five generations, such as fifteen generations, preferably thirty generations. Generally such a polynucleotide would be inherited by both daughter cells every generation.
The polynucleotide may comprise a promoter or an origin of replication (e.g. upstream of any sequences encoding a replication protein).
The polynucleotide of the invention can be transformed or transfected into a bacterium, such as a Propionibacterium, or E. coli, for example by a suitable method11. It may be present in a bacterium at a copy number of 5 to 500, such as 10 to 100.
The polynucleotide may be capable of autonomous replication in a bacterium other than a Propionibacterium. Such a bacterium may be E. coli or a gram positive or G:C rich bacterium or one of the class Actinomycetes. Such a polynucleotide will generally comprise sequences which enable the polynucleotide to be autonomously replicated in that bacterium. Such sequences can be derived from plasmids which are able to replicate in that bacterium.
A polynucleotide of the invention may be one which has been produced by replication in a Propionibacterium. Alternatively it may have been produced by replication in another bacterium such as E. coli. The polynucleotide may be able to circumvent the host restriction systems of Propionibacterium. 
Vectors
A second aspect of the invention relates to a vector comprising a polynucleotide of the first aspect. The vector may be capable of replication in a host cell, such as a bacterium, for examples Actinomycetes, e.g. Propionibacterium or, E. coli. The vector may be a linear polynucleotide or, more usually, a circular polynucleotide. The vector may be a hybrid of the polynucleotide of the invention and another vector. The other vector may be an E. coli vector, such as pBR322, or a vector of the pUC family, R1, ColD or RSF1010 or a vector derived therefrom.
The polynucleotide or vector of the invention may be a plasmid. Such a plasmid may have a restriction map the same as or substantially similar to the restriction maps shown in FIG. 1, 2a or 2b. 
The polynucleotide or vector may have a size of 1 kb to 20 kb, such as from 2 to 10 kb, optimally from 3 to 7 kb.
The polynucleotide or vector may comprise multiple functional cloning sites. Such cloning sites generally comprise the recognition sequence of restriction enzymes. The polynucleotide or vector may comprise the sequence shown in SEQ ID No: 1 and/or contains restriction enzyme recognition sites for EcoRI, SacI, AlwNI, BsmI, BsaBI, BclI, ApaI, HindIII. SalI, HpaI, PstI, SphI, BamHI, A651, EcoRV and BglII. The polynucleotide or vectors may thus comprise one, more than one or all of these restriction enzyme sites, generally in the order shown in the Figures.
Preferably, when present in a bacterium such as a Propionibacterium or E. coli, the polynucleotide or vector of the invention does not integrate into the chromosome of the bacterium. Generally the polynucleotide or vector does not integrate within 5 generations, preferably 20 or 30 grunions.
The polynucleotide or vector may be an autonomously replicating plasmid that can remain extrachromosomal inside a host cell, which plasmid is derived from an (to the host) is capable of expressing that gene inside the host cell. The term xe2x80x9cderived fromxe2x80x9d means that the autonomously replicating plasmid includes a sequence the same as the polynucleotide of the invention.
The vector of the invention may comprise a selectable marker. The selectable marker may be one which confers antibiotic resistance, such as ampicillin kanamycin or teracylin resistance genes. The selectable marker may be an erythromycin resistance gene. The erythromycin resistance gene may be from Actinomycetes such as Saccharopolyspora erythraea, for example from Saccharopolyspora erythraea NRKL2338. Other selectable markers which may be present in the vector include genes conferring resistance to chloraphenicol, thiostreptomycin, viomycin, ncomycin apramycin, hygromycin, bicomycin or streptomycin.
The vector may be an expression vector, and so may comprise a heterologous gene (which does not generally occur in the host cell, e.g. Propionibacteria), or an endogenous or homologous gene of the host e.g. Propionibacteria. In the expression vector the gene to be expressed is usually operably linked to a control sequence which is capable of providing for the expression of the gene in a host cell.
The term xe2x80x9coperably linkedxe2x80x9d refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A controlled sequence xe2x80x9coperably linkedxe2x80x9d to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences.
The heterologous or endogenous gene may be inserted between nucleotides 1 and 200 or between nucleotides 1500 to 3555 of SEQ ID No:1 or at an equivalent position in a homologous polynucleotide.
Such genes may comprise homologous or endogenous genes such as for elongation factors, promoters regulatory sequences or elements, and replication proteins. Other genes (which may be heterologous to the host) include those encoding for or assisting in the production of nutritional factors immmomodulators, hormones, proteins and enzymes (e.g. protease, amylases, peptidases, lipases), texturing agents, flavouring substances (e.g. diactyl, actonc), gene clusters antimicrobial agents (e.g. nisin), substances for use in foodstuffs (e.g. in sausages, cheese) metabolic enzymes, vitamins (e.g. B12), uroporphyrinogen (III) methyltransferase (UP III MT), cobA, antigens and (e.g. for vaccines) therapeutic agents. As will be seen the hosts can produce a wide variety of substance not just polypeptides, which may be either the desired product or may be used to produce the desired product.
The heterologous gene may have a therapeutic effect on a human or animal. Such a gene may comprise an antigen for example from a pathogenic organism. The host, such as Propionibacterium, comprising a polynucleotide with such a heterologous gene may be used as or in a vaccine, and may provide protection against the pathogens.
The heterologous antigen may be a complete protein or a part of a protein containing an epitope. The antigen may be from a bacterium, a virus, a yeast or a fungus.
Host Cells and Expression
The host cell forms the third aspect of the invention and comprise a polynucleotide or vector of the first or second aspect. The host cell may be a bacterium e.g. of the class Actinomrycetes. The bacterium may be a Propionibacterium or E. coli. The Propionibacterium may be P. freudenreichii, P. jensenii, P. thoenii or P. acidipropionici. 
In a fourth aspect the invention provides a process for producing a host cell of the third aspect, the process comprising transforming or transfecting a host cell with a polynucleotide or vector of the first or second aspect, e.g. with known formation techniques11.
In a fifth aspect the invention provides a process for the preparation of a polypeptide encoded by the polynucleotide or vector of invention present in host cell of the invention comprising placing or culturing the host cell in conditions where expression of the polypeptide occur.
This aspect of the invention thus provides a process for the preparation of a polypeptide encoded by a given gene, which process comprises cultivating a host cell transformed or transfected with an expression vector comprising the gene, under conditions to provide for an expression of the said polypeptide, and optionally recovering the expressed polypeptide. The host cell may be of the class Actinomycetes, or a gram positive bacteria such as Propionibacterium or E. coli. 
Promoters, translation initiators, translation terminators, elongation factor genes, ribosomal. RNA, antibiotic resistance genes, synthetic promoters (e.g. designed on consensus sequences) to other expression regulation signals present in the polynucleotide or vector can be those which are compatible with expression in the host cell. Such promoters include the promoters of the endogenous gene: of the host coll.
Culturing conditions may be aerobic or anaerobic conditions depending an the host. For a fermentation process the host cell would be placed in anaerobic, and then possibly aerobic conditions. The compound produced, such as an exposed polypeptide, may then be recovered, e.g. from the host cell or fermentation medium. The expressed polypeptide may be secreted from the host cell. Alternatively the polypeptide may not be secreted from the host cell. In such a case the polypeptide may be expressed on the source of the host cell. This may be desirable, for example, if the polypeptide comprises an antigen to which an immune response is desired in human or animal
A homologous gene that may be present in the vector of the invention may be cobA. A host cell vector may therefore be capable of producing a compound such as vitamin B12, from a substrate or the compound may be the product of an enzyme. The invention specifically provides a process for the preparation of vitamin B12 comprising cultivating or fermenting such a host cell under conditions in which the UP(III) MT gene is expressed. The expressed enzyme can be contacted with a suitable substrate under conditions in which the substrate is converted to vitamin B12. This may result in increased production of vitamin B12.
Therapeutics
As described above the polynucleotide of the invention may comprise a heterologous gene which is a therapeutic gene. Thus the invention includes a host cell comprising a vector of the invention which comprises a therapeutic gene for use is a method of treatment of the human or animal body by therapy. Such a host cell may be Propionibacterium. The host cell may be alive or dead,
The host cell can be formulated for clinical administration by mixing them with a pharmaceutically acceptable carrier or diluent. For example they can be formulated for topical, parenteral, intravenous, intramuscular, subcutaneous, oral or transdermal administration. The host call may be mixed with any vehicle which is pharmaceutically acceptable and appropriate for the desired route of administration. The pharmaceutically acceptable carrier or diluent for injection may be, for example, a sterile or isotonic solution such as Water for injection or physiological saline.
The dose of the host cells may be adjusted according to various parameters, especially according to the type of the host cells used, the age, weight and condition of the patient to be treated; the mode of administration used; the condition to be treated; and the required clinical regimen. As a guide, the number of host cells administered, for example by oral administration, is from 107 to 1011 host cells per dose for a 70 kg adult human.
The routes of administration and dosages described are intended only as a guide since a skilled practitioner will be able to determine readily the optimum route of administration and dosage of any particular patient and condition.
Polypeptides
A six aspect of the invention provides a polypeptide of the invention comprising one of the amino acid sequences setout in SEQ ID NO: 2 or 3 or a substantially homologous sequence or of a fragment of either of these sequences, the polypeptide may be one encoded by a polynucleotide of the first aspect. In general, the naturally occurring amino acid sequences shown in SEQ ID NO: 2 or 3 are preferred. However, the polypeptides of the invention include homologues of the natural sequences, and fragments of the natural sequences and their homologues, which have the activity of the naturally occurring polypeptide. One such activity may be to effect the replication of the polynucleotide of the invention. In particular, a polypeptide of the invention may comprise:
(a) the protein of SEQ ID No: 2 or 3; or
(b) a homologue thereof from Actinomycetes, such as Propionibacterium freudenreichii or other Propionibacterium strains or
(c) a protein at least 70% homologous to (a) or (b).
A homologue may occur naturally in a Propionibacterium and may function in a substantially similar manner to a polypeptide of SEQ ID NO: 2 or 3. Such a homologue may occur in Actinomycetes or gram positive bacteria.
A protein at least 70% homologous to the protein of SEQ ID NO: 2 or 3 or a homologue thereof will be preferably at least go or 90% and more preferably at least 95%, 97% or 99% homologous thereto over a region of at least 20, preferably at least 30, for instance at least 40, 60 or 100 or more contiguous amino acids. Methods of measuring protein homology are well known in the art and it will be understood by those of skill in the art that in the present context homology is calculated on the basis of amino acid identity (sometimes referred to as xe2x80x9chard homologyxe2x80x9d).
The sequences of the proteins of SEQ ID NO: 2 and 3 and of homologues can thus be modified to provide other polypeptides within the invention.
Amino acid substitutions may be made, for example from 1, 2 or 3 to 10, 20 or 30 substitutions. The modified polypeptide generally retains its natural activity. Conservative substitutions may be made, for example according to the following Table. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other.
Polypeptides of the invention also include fragments of the above-mentioned full length polypeptides and variants thereof, including fragments of the sequences set out in SEQ ID NO: 2 or 3. Such fragments can retain the natural activity of the full-length polypeptide.
Suitable fragments will be at about 5, e.g. 10, 12, 15 or 20 amino acids in size. Polypeptide fragments of SEQ ID No: 2 and 3 and homologues thereof may contain one or more (e.g. 2, 3, 5, or 10) substitutions, deletions or insertions, including conserved substitutions.
Polypeptides of the invention may be in a substantially isolated form. A polypeptide of the invention may also be in a substantially purified form, in which case it will generally comprise the polypeptide in a preparation in which more than 90%, e.g. 95% 98% or 99% of the polypeptide in the preparation is a polypeptide of the invention.
A polypeptide of the invention may be labelled with a revealing label. The revealing label may be any suitable label which allows the polypeptide to be detected. Suitable labels include radioisotopes, e.g. 125I, 35S, enzymes, antibodies, polynucleotides and linkers such as biotin.
As will be apparent from the discussion, the host cells of the third aspect can be used to produce not only the recombinant proteins, but also other compounds of interest, including non-proteins such as inorganic chemicals, in particular vitamins. A seventh aspect of the present invention therefore relates to a process for the production of a compound, the process comprising culturing or fermenting host cells of the third aspect under condition whereby the desired compound is produced. Although this compound may be a polypeptide, for example a polypeptide of the sixth aspect, it may also be one of the compounds mentioned in the previous discussion concerning genes to be expressed. Clearly inorganic compounds will not be expressed by a gene, but they may be produced by an enzyme or the polypeptide or enzyme may assist the host cell in the production of the desired compound. These compounds may be produced inside the cell, and later isolated, for example following lysis of the host call or they may pass through the wall of the host cell into a surrounding medium, which may be a fermentation medium for example an aqueous solution. In this way the host cells can be cultured in an aqueous medium that comprises cells and nutrients for the cells, for example assimiable sources of carbon and/or nitrogen.
The polypeptides so produced may have therapeutic uses. They may be drugs or other pharmacologically active compounds, or may be antigenic or immunogenic, in which case they may find use in vaccines.
The invention additionally encompasses compounds produced by this process, whether or not it is a recombinant polypeptide. Compounds specifically contemplated are vitamins, such as vitamin B12 (cobalamin).
In some cases the compound need not be isolated either from the fermentation medium or from the host cells. The host cells may themselves be used in particular applications, for example in, or in the manufacturing of, foodstuffs such as sausages, or in cheese makings or the host cells may for example be included in an animal feed such as when the host cells contain compound to be ingested by the animal in question. The invention therefor extends to the use of these compounds or the host cells in the production of foodstuffs such as cheeses and sausages. The invention also contemplates foodstuffs or animal feed comprising host cell or a compound produced by the invention.
In a particularly preferred embodiment of the present invention the host cells can be used in a cheese making process, and so the invention additionally includes a process for manufacturing cheeses where the microorganism employed are host cells of the invention. The host cells may be used instead of or in addition to, other bacteria, such as lactic acid bacteria. Propionic acid bacteria are currently used in cheese making processes, for example with mesophilic cultures type of cheese) as well as thermophilic cultures (Emmental). Both mesophilic and thermophilic organisms can be responsible for the acidification of the milk or cheese. In this way the host cells of the invention can be not only used for cheese but also for the production of other family dairy products (e.g. yoghurts). Propionic acid bacterium are employed in cheese making because of their ability to convert lactate and carbohydrates to propionic acid, acetic acid and carbon dioxide. The host cells of the invention, especially if they are propionibacteria, can be employed because they can be less sensitive to nitrates and salt, which may allow the reduction or omission of bactofugation of the milk (usually employed to reduce the levels of Clostridia).
The fermentation of the host cells may have one or two phases or stages. These may be for example a growth and/or production phase, or anaerobic and/or aerobic phase. Preferably, there will be a growth and/or anaerobic phase, and suitable also (e.g. afterwards) a production and/or aerobic phase.
Both the carbon and/or nitrogen sources may be complex sources or individual compounds. For carbon, it is preferred that this is glucose. For nitrogen, appropriate sources include yeast extract or ammonia or ammonium ions.
Preferred features and characteristics of one aspect of the invention are suitable for another aspect mutatis mutandis.